Hi - yes, you are using the wrong transform in the second command. You
want to invert the DTI->mprage transform (a.mat) using InvertXFM_gui
or convert_xfm and use this inverted transform instead of ident.mat in
the second command.
Cheers.
On 7 Apr 2008, at 09:25, Ravi Shetty wrote:
> /Applications/fsl/bin/flirt -in
> /Users/IMAC/Desktop/Nifti/itamar/dti_FA.nii.gz -ref
> /Users/IMAC/Desktop/Nifti/itamar/newmprage_brain.nii.gz -out
> /Users/IMAC/Desktop/a -omat /Users/IMAC/Desktop/a.mat -bins 256 -cost
> corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 6 -
> interp
> trilinear
>
> /Applications/fsl/bin/flirt -in
> /Users/IMAC/Desktop/Nifti/itamar/newmprage-mask.nii.gz -applyxfm -init
> /Applications/fsl/etc/flirtsch/ident.mat -out /Users/IMAC/Desktop/b
> -paddingsize 0.0 -interp trilinear -ref
> /Users/IMAC/Desktop/Nifti/itamar/dti_FA.nii.gz
>
>
> I am using the FLIRT gui but here are the commands that print out. I
> have
> checked the orientations and they are all in radiological
> orientation. In
> this particular case the CC ROI that I created in T1 space appears
> directly
> above the CC in diffusion space. So it is only off in terms of where
> it
> should be in the superior-inferior plane but is dead on in terms of
> the
> other 2 planes. Thanks again.
>
>
> On Mon, 7 Apr 2008 08:25:01 +0100, Mark Jenkinson
> <[log in to unmask]> wrote:
>
>> Hi,
>>
>> We need more information than this to diagnose the error.
>> Can you send us the exact fsl command-lines that you are running?
>>
>> And also check if all your images are in "radiological" orientation
>> as determined by fslorient. This can cause problems if you have
>> a mix of "radiological" and "neurological".
>>
>> All the best,
>> Mark
>>
>>
>> On 7 Apr 2008, at 03:03, Ravi Shetty wrote:
>>
>>> Hi I have been using FLIRT to register my T1 and DTI images to each
>>> other but keep running into
>>> problems. The registered images produced are always very close to
>>> what they should be when I
>>> overlay them onto the T1 image. The problem I have is the matrixes
>>> don't always reflect the
>>> registration image. I create a CC ROI mask on the T1 image/
>>> registered image and use the matrix I
>>> produced to convert it back into difusion space. Now when I do this
>>> with some subjects the ROI will
>>> be spot on the CC and for others it will be off somewhere in the
>>> cortex or even just into the black
>>> void. I can't seem to find any rhyme or reason for this and the
>>> variation of how off the matrix is does
>>> not seem to be consistent, any help figuring this out would be
>>> appreciated. Thanks.
>>>
>> =
>> =
>> =
>> =
>> =====================================================================
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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